(Q34590458)

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DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

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scholarly article

1 reference

Europe PubMed Central

3 August 2017

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly (English)

1 reference

Europe PubMed Central

3 August 2017

whole genome sequencing

1 reference

based on heuristic

inferred from title

15

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Europe PubMed Central

3 August 2017

Pieter Wesseling

12

object named as

Pieter Wesseling

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Europe PubMed Central

3 August 2017

2

object named as

Daoud Sie

1 reference

Europe PubMed Central

3 August 2017

Jaap C Reijneveld

11

object named as

Jaap C Reijneveld

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Europe PubMed Central

3 August 2017

10

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Gerrit A Meijer

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Europe PubMed Central

3 August 2017

author name string

Ilari Scheinin

1

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Europe PubMed Central

3 August 2017

Henrik Bengtsson

3

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Europe PubMed Central

3 August 2017

Mark A van de Wiel

4

1 reference

Europe PubMed Central

3 August 2017

Adam B Olshen

5

1 reference

Europe PubMed Central

3 August 2017

Hinke F van Thuijl

6

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Europe PubMed Central

3 August 2017

Hendrik F van Essen

7

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Europe PubMed Central

3 August 2017

Paul P Eijk

8

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Europe PubMed Central

3 August 2017

François Rustenburg

9

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Europe PubMed Central

3 August 2017

Daniel Pinkel

13

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3 August 2017

Donna G Albertson

14

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3 August 2017

language of work or name

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publication date

18 September 2014

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3 August 2017

Genome Research

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3 August 2017

24

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3 August 2017

12

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Europe PubMed Central

3 August 2017

2022-2032

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Europe PubMed Central

3 August 2017

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas

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CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data

1 reference

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7 July 2018

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ENCODE data in the UCSC Genome Browser: year 5 update

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An integrated map of genetic variation from 1,092 human genomes

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Genetics and pharmacogenomics of diffuse gliomas

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An integrated encyclopedia of DNA elements in the human genome

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Statistical challenges associated with detecting copy number variations with next-generation sequencing.

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Fast gapped-read alignment with Bowtie 2

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Summarizing and correcting the GC content bias in high-throughput sequencing

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Fast computation and applications of genome mappability

1 reference

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7 July 2018

High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues

1 reference

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7 July 2018

CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material

1 reference

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Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis.

1 reference

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7 July 2018

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

1 reference

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7 July 2018

Genomic aberrations in pediatric diffuse intrinsic pontine gliomas

1 reference

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7 July 2018

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

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7 July 2018

Chipster: user-friendly analysis software for microarray and other high-throughput data

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Hallmarks of Cancer: The Next Generation

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7 July 2018

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

The European Nucleotide Archive

1 reference

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7 July 2018

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

1 reference

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7 July 2018

Preprocessing and downstream analysis of microarray DNA copy number profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

De novo assembly of human genomes with massively parallel short read sequencing

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples

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7 July 2018

The Sequence Alignment/Map format and SAMtools

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7 July 2018

Fast and accurate short read alignment with Burrows-Wheeler transform

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7 July 2018

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

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7 July 2018

High-resolution mapping of copy-number alterations with massively parallel sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

The fine-scale and complex architecture of human copy-number variation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

Tissue preparation: Tissue issues

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7 July 2018

A faster circular binary segmentation algorithm for the analysis of array CGH data

1 reference

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7 July 2018

BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)

1 reference

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Structural variation in the human genome

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7 July 2018

Bioconductor: open software development for computational biology and bioinformatics

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7 July 2018

The human genome browser at UCSC

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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

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7 July 2018

Assembly of microarrays for genome-wide measurement of DNA copy number

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

7 July 2018

High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4248318

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CGHcall: calling aberrations for array CGH tumor profiles.

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Smoothing waves in array CGH tumor profiles

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Pathology databanking and biobanking in The Netherlands, a central role for PALGA, the nationwide histopathology and cytopathology data network and archive.

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Detection limits of DNA copy number alterations in heterogeneous cell populations

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12 December 2020

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Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray

1 reference

https://pubmed.ncbi.nlm.nih.gov/25236618

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1101/GR.175141.114

1 reference

Europe PubMed Central

3 August 2017

1 reference

Europe PubMed Central

3 August 2017

1 reference

Europe PubMed Central

3 August 2017

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